Multiple sequence alignment - TraesCS7D01G102800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G102800 chr7D 100.000 3616 0 0 1 3616 62261726 62258111 0.000000e+00 6678
1 TraesCS7D01G102800 chr7D 96.314 2062 62 6 1405 3452 62107387 62105326 0.000000e+00 3374
2 TraesCS7D01G102800 chr7D 79.575 1743 314 29 1005 2710 62280041 62281778 0.000000e+00 1208
3 TraesCS7D01G102800 chr7D 81.790 1285 226 6 1187 2467 60705381 60704101 0.000000e+00 1070
4 TraesCS7D01G102800 chr7D 80.558 1291 243 6 1181 2467 61228734 61227448 0.000000e+00 987
5 TraesCS7D01G102800 chr7D 95.627 343 14 1 236 578 62112227 62111886 1.900000e-152 549
6 TraesCS7D01G102800 chr7D 93.075 361 5 1 1060 1420 62107769 62107429 8.960000e-141 510
7 TraesCS7D01G102800 chr7D 88.398 362 15 6 680 1035 62111889 62111549 9.340000e-111 411
8 TraesCS7D01G102800 chr7D 93.522 247 16 0 2 248 62112491 62112245 5.700000e-98 368
9 TraesCS7D01G102800 chr7D 99.138 116 1 0 3492 3607 62105328 62105213 3.660000e-50 209
10 TraesCS7D01G102800 chr7D 93.162 117 8 0 568 684 94444321 94444437 4.800000e-39 172
11 TraesCS7D01G102800 chr7A 91.732 2673 180 19 678 3340 65330287 65327646 0.000000e+00 3674
12 TraesCS7D01G102800 chr7A 80.228 1578 279 22 1167 2715 65441960 65443533 0.000000e+00 1155
13 TraesCS7D01G102800 chr7A 80.620 1290 244 6 1181 2467 65154646 65153360 0.000000e+00 992
14 TraesCS7D01G102800 chr7A 91.111 360 17 8 2 355 65331496 65331146 1.180000e-129 473
15 TraesCS7D01G102800 chr7A 90.459 283 22 3 3335 3616 65325901 65325623 5.700000e-98 368
16 TraesCS7D01G102800 chr7A 91.701 241 20 0 338 578 65330522 65330282 5.790000e-88 335
17 TraesCS7D01G102800 chr7A 94.643 112 6 0 575 686 109580610 109580499 1.330000e-39 174
18 TraesCS7D01G102800 chr7A 82.759 116 19 1 2747 2862 711459156 711459270 6.390000e-18 102
19 TraesCS7D01G102800 chr7B 82.710 1284 220 2 1185 2467 3342356 3341074 0.000000e+00 1140
20 TraesCS7D01G102800 chr7B 94.872 117 6 0 566 682 555654391 555654507 2.220000e-42 183
21 TraesCS7D01G102800 chr7B 96.330 109 4 0 574 682 680913362 680913470 2.870000e-41 180
22 TraesCS7D01G102800 chr7B 95.370 108 5 0 575 682 693255331 693255224 4.800000e-39 172
23 TraesCS7D01G102800 chr2D 80.843 1258 233 8 1236 2489 601263807 601262554 0.000000e+00 981
24 TraesCS7D01G102800 chr2D 93.966 116 6 1 569 684 621124840 621124726 1.330000e-39 174
25 TraesCS7D01G102800 chr2A 93.913 115 6 1 573 687 635580061 635579948 4.800000e-39 172
26 TraesCS7D01G102800 chr2A 87.857 140 12 4 575 712 707748412 707748276 3.740000e-35 159
27 TraesCS7D01G102800 chr2A 80.714 140 24 3 2747 2884 306689249 306689111 4.940000e-19 106
28 TraesCS7D01G102800 chr4A 91.597 119 8 2 575 692 617363045 617362928 2.890000e-36 163
29 TraesCS7D01G102800 chr6B 84.768 151 14 5 2768 2916 192934612 192934469 3.760000e-30 143


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G102800 chr7D 62258111 62261726 3615 True 6678.0 6678 100.000000 1 3616 1 chr7D.!!$R3 3615
1 TraesCS7D01G102800 chr7D 62280041 62281778 1737 False 1208.0 1208 79.575000 1005 2710 1 chr7D.!!$F1 1705
2 TraesCS7D01G102800 chr7D 60704101 60705381 1280 True 1070.0 1070 81.790000 1187 2467 1 chr7D.!!$R1 1280
3 TraesCS7D01G102800 chr7D 61227448 61228734 1286 True 987.0 987 80.558000 1181 2467 1 chr7D.!!$R2 1286
4 TraesCS7D01G102800 chr7D 62105213 62112491 7278 True 903.5 3374 94.345667 2 3607 6 chr7D.!!$R4 3605
5 TraesCS7D01G102800 chr7A 65325623 65331496 5873 True 1212.5 3674 91.250750 2 3616 4 chr7A.!!$R3 3614
6 TraesCS7D01G102800 chr7A 65441960 65443533 1573 False 1155.0 1155 80.228000 1167 2715 1 chr7A.!!$F1 1548
7 TraesCS7D01G102800 chr7A 65153360 65154646 1286 True 992.0 992 80.620000 1181 2467 1 chr7A.!!$R1 1286
8 TraesCS7D01G102800 chr7B 3341074 3342356 1282 True 1140.0 1140 82.710000 1185 2467 1 chr7B.!!$R1 1282
9 TraesCS7D01G102800 chr2D 601262554 601263807 1253 True 981.0 981 80.843000 1236 2489 1 chr2D.!!$R1 1253

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
591 1265 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 F
729 1403 0.609131 CATTTGCGAGGTCCACCCTT 60.609 55.000 0.00 0.00 46.51 3.95 F
1233 5671 1.204704 TCTACTGACCATCACCGCAAG 59.795 52.381 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 6342 1.071471 AACTTCGCCACTCCACCTG 59.929 57.895 0.0 0.0 0.0 4.00 R
2580 7114 1.530323 AGTTTGATACACCCGCCAAC 58.470 50.000 0.0 0.0 0.0 3.77 R
3046 7601 0.257039 AGACATGACCCATCCTTGCC 59.743 55.000 0.0 0.0 0.0 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.459063 GCCCGTAAGAGCGACCCT 61.459 66.667 0.00 0.00 43.02 4.34
38 39 2.123428 GCGACCCTAGGAACGGCTA 61.123 63.158 22.11 0.00 0.00 3.93
161 163 0.898320 CCTGAGTCGAAGGTCCATGT 59.102 55.000 0.00 0.00 0.00 3.21
226 228 5.296151 ACAACAGGTGAAAGATGAGAAGA 57.704 39.130 0.00 0.00 0.00 2.87
341 373 2.661675 CGAGTCAAGTTCATGTACCACG 59.338 50.000 0.00 0.00 0.00 4.94
343 375 2.367567 AGTCAAGTTCATGTACCACGGT 59.632 45.455 0.00 0.00 0.00 4.83
428 1102 6.912591 GGCACAATTATCTCGTAAAAGGATTG 59.087 38.462 0.00 0.00 0.00 2.67
431 1105 7.846107 CACAATTATCTCGTAAAAGGATTGTCG 59.154 37.037 0.00 0.00 0.00 4.35
507 1181 3.731652 TGGTTGAAGATGCAACTTTGG 57.268 42.857 10.85 0.00 45.64 3.28
513 1187 5.787953 TGAAGATGCAACTTTGGAAATGA 57.212 34.783 10.85 0.00 30.51 2.57
546 1220 6.014669 CCCATCCCAAAGAAGTGAAAAATGTA 60.015 38.462 0.00 0.00 0.00 2.29
584 1258 9.828039 AAAATAAAATACTTAGTACTCCCTCCG 57.172 33.333 0.00 0.00 0.00 4.63
585 1259 8.544687 AATAAAATACTTAGTACTCCCTCCGT 57.455 34.615 0.00 0.00 0.00 4.69
586 1260 6.864151 AAAATACTTAGTACTCCCTCCGTT 57.136 37.500 0.00 0.00 0.00 4.44
587 1261 6.462552 AAATACTTAGTACTCCCTCCGTTC 57.537 41.667 0.00 0.00 0.00 3.95
588 1262 2.363683 ACTTAGTACTCCCTCCGTTCG 58.636 52.381 0.00 0.00 0.00 3.95
589 1263 1.674962 CTTAGTACTCCCTCCGTTCGG 59.325 57.143 0.00 4.74 0.00 4.30
590 1264 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
591 1265 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
592 1266 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
593 1267 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
594 1268 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
595 1269 1.755380 ACTCCCTCCGTTCGGAATTAG 59.245 52.381 14.79 13.09 33.41 1.73
596 1270 1.755380 CTCCCTCCGTTCGGAATTAGT 59.245 52.381 14.79 0.00 33.41 2.24
597 1271 2.167900 CTCCCTCCGTTCGGAATTAGTT 59.832 50.000 14.79 0.00 33.41 2.24
598 1272 2.093869 TCCCTCCGTTCGGAATTAGTTG 60.094 50.000 14.79 1.97 33.41 3.16
599 1273 2.354403 CCCTCCGTTCGGAATTAGTTGT 60.354 50.000 14.79 0.00 33.41 3.32
600 1274 2.928116 CCTCCGTTCGGAATTAGTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
601 1275 3.368116 CCTCCGTTCGGAATTAGTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
602 1276 3.841643 TCCGTTCGGAATTAGTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
603 1277 2.597305 CCGTTCGGAATTAGTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
604 1278 3.495193 CGTTCGGAATTAGTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
605 1279 3.916172 CGTTCGGAATTAGTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
606 1280 4.383649 CGTTCGGAATTAGTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
607 1281 5.107760 CGTTCGGAATTAGTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
608 1282 6.400727 CGTTCGGAATTAGTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
609 1283 6.403333 TCGGAATTAGTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
610 1284 5.350365 TCGGAATTAGTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
611 1285 5.350365 CGGAATTAGTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
612 1286 6.037172 CGGAATTAGTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
613 1287 7.189512 GGAATTAGTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
614 1288 7.148239 GGAATTAGTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
615 1289 8.786826 AATTAGTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
616 1290 8.964476 ATTAGTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
617 1291 6.910536 AGTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
618 1292 6.644347 AGTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
619 1293 7.782049 AGTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
620 1294 8.258007 AGTTGTCTCGAAAATGGATGTATCTAA 58.742 33.333 0.00 0.00 0.00 2.10
621 1295 8.879759 GTTGTCTCGAAAATGGATGTATCTAAA 58.120 33.333 0.00 0.00 0.00 1.85
622 1296 9.443323 TTGTCTCGAAAATGGATGTATCTAAAA 57.557 29.630 0.00 0.00 0.00 1.52
623 1297 8.879759 TGTCTCGAAAATGGATGTATCTAAAAC 58.120 33.333 0.00 0.00 0.00 2.43
624 1298 9.099454 GTCTCGAAAATGGATGTATCTAAAACT 57.901 33.333 0.00 0.00 0.00 2.66
653 1327 6.604735 ACGTCTAAATACATCCATTTCTGC 57.395 37.500 0.00 0.00 30.84 4.26
654 1328 5.234329 ACGTCTAAATACATCCATTTCTGCG 59.766 40.000 0.00 0.00 30.84 5.18
655 1329 5.462068 CGTCTAAATACATCCATTTCTGCGA 59.538 40.000 0.00 0.00 30.84 5.10
656 1330 6.146184 CGTCTAAATACATCCATTTCTGCGAT 59.854 38.462 0.00 0.00 30.84 4.58
657 1331 7.328493 CGTCTAAATACATCCATTTCTGCGATA 59.672 37.037 0.00 0.00 30.84 2.92
658 1332 8.988934 GTCTAAATACATCCATTTCTGCGATAA 58.011 33.333 0.00 0.00 30.84 1.75
659 1333 9.554395 TCTAAATACATCCATTTCTGCGATAAA 57.446 29.630 0.00 0.00 30.84 1.40
666 1340 8.299570 ACATCCATTTCTGCGATAAATAATTCC 58.700 33.333 0.00 0.00 0.00 3.01
667 1341 6.898041 TCCATTTCTGCGATAAATAATTCCG 58.102 36.000 0.00 0.00 0.00 4.30
668 1342 6.708502 TCCATTTCTGCGATAAATAATTCCGA 59.291 34.615 0.00 0.00 0.00 4.55
669 1343 7.227711 TCCATTTCTGCGATAAATAATTCCGAA 59.772 33.333 0.00 0.00 0.00 4.30
670 1344 7.323656 CCATTTCTGCGATAAATAATTCCGAAC 59.676 37.037 0.00 0.00 0.00 3.95
671 1345 5.570262 TCTGCGATAAATAATTCCGAACG 57.430 39.130 0.00 0.00 0.00 3.95
672 1346 4.446385 TCTGCGATAAATAATTCCGAACGG 59.554 41.667 6.94 6.94 0.00 4.44
673 1347 4.370049 TGCGATAAATAATTCCGAACGGA 58.630 39.130 12.04 12.04 43.52 4.69
674 1348 4.446385 TGCGATAAATAATTCCGAACGGAG 59.554 41.667 15.34 2.36 46.06 4.63
675 1349 4.143179 GCGATAAATAATTCCGAACGGAGG 60.143 45.833 15.34 0.00 46.06 4.30
676 1350 4.387862 CGATAAATAATTCCGAACGGAGGG 59.612 45.833 15.34 0.00 46.06 4.30
677 1351 3.918294 AAATAATTCCGAACGGAGGGA 57.082 42.857 15.34 2.49 46.06 4.20
683 1357 0.911769 TCCGAACGGAGGGAGTACTA 59.088 55.000 12.04 0.00 39.76 1.82
685 1359 2.092212 TCCGAACGGAGGGAGTACTATT 60.092 50.000 12.04 0.00 39.76 1.73
704 1378 1.882912 TGATGCAATAGGGATGACGC 58.117 50.000 0.00 0.00 0.00 5.19
729 1403 0.609131 CATTTGCGAGGTCCACCCTT 60.609 55.000 0.00 0.00 46.51 3.95
866 1541 5.524646 AGCTTGATGTGAAAAACATGGTTTG 59.475 36.000 10.04 0.00 44.51 2.93
939 1614 2.939640 TGGAAGGTCCCGTACGTAGTAC 60.940 54.545 15.21 6.28 46.40 2.73
1034 1713 5.365025 ACCTCTGCATTCACATAGACTACAT 59.635 40.000 0.00 0.00 0.00 2.29
1039 1718 4.752101 GCATTCACATAGACTACATCACCC 59.248 45.833 0.00 0.00 0.00 4.61
1042 1721 6.560003 TTCACATAGACTACATCACCCAAT 57.440 37.500 0.00 0.00 0.00 3.16
1191 5629 1.697982 ACCCGGAGCTATTTATCCCAC 59.302 52.381 0.73 0.00 31.43 4.61
1196 5634 2.550208 GGAGCTATTTATCCCACCCACG 60.550 54.545 0.00 0.00 0.00 4.94
1233 5671 1.204704 TCTACTGACCATCACCGCAAG 59.795 52.381 0.00 0.00 0.00 4.01
1368 5826 7.927092 TCTCTCATCTTTGCTTGATGATTCTAG 59.073 37.037 13.98 10.61 46.01 2.43
1663 6178 3.427573 TCGTGTAATGAACCTCTCAGGA 58.572 45.455 0.00 0.00 37.67 3.86
1687 6202 4.584688 TGCTCTGCATCAGTGACG 57.415 55.556 0.00 0.00 31.71 4.35
1771 6286 2.883828 AACAGAGACCACTGGGCCG 61.884 63.158 0.00 0.00 41.59 6.13
1827 6342 3.202906 TGCCTAACATCTTATTCCGCAC 58.797 45.455 0.00 0.00 0.00 5.34
2227 6742 4.517285 GTGGCCTCAATCTATCAGACAAA 58.483 43.478 3.32 0.00 0.00 2.83
2726 7271 9.026121 CCAAATAGTAGTACAGTGGCTATATCT 57.974 37.037 2.52 0.00 0.00 1.98
2764 7316 1.298859 CCAGCTCGTTTGGCACCTAC 61.299 60.000 0.00 0.00 0.00 3.18
2800 7352 6.410038 GTTTTGTGGAAATGACATGAAAACG 58.590 36.000 0.00 0.00 30.49 3.60
2916 7470 0.388134 CATGTGCTGTTTGGCTGCTC 60.388 55.000 0.00 0.00 41.79 4.26
3085 7640 4.162509 GTCTAGGGTCTAGAAGGCACAAAT 59.837 45.833 6.26 0.00 0.00 2.32
3204 7759 4.761739 TGAATTAGGCAAGTTCTGGACAAG 59.238 41.667 0.00 0.00 0.00 3.16
3377 9682 9.781633 TGTAAGAAAACTGGCTAATGTAGTTAA 57.218 29.630 0.00 0.00 33.82 2.01
3429 9735 5.240844 CCGGACCAATATTTTAGTTCCATCC 59.759 44.000 0.00 0.00 0.00 3.51
3449 9755 7.936847 TCCATCCTGTAAAAGCATCGTAATATT 59.063 33.333 0.00 0.00 0.00 1.28
3450 9756 8.017373 CCATCCTGTAAAAGCATCGTAATATTG 58.983 37.037 0.00 0.00 0.00 1.90
3451 9757 8.773645 CATCCTGTAAAAGCATCGTAATATTGA 58.226 33.333 0.00 0.00 0.00 2.57
3452 9758 8.902540 TCCTGTAAAAGCATCGTAATATTGAT 57.097 30.769 0.00 0.00 0.00 2.57
3453 9759 8.988934 TCCTGTAAAAGCATCGTAATATTGATC 58.011 33.333 0.00 0.00 0.00 2.92
3454 9760 8.773645 CCTGTAAAAGCATCGTAATATTGATCA 58.226 33.333 0.00 0.00 0.00 2.92
3455 9761 9.586150 CTGTAAAAGCATCGTAATATTGATCAC 57.414 33.333 0.00 0.00 0.00 3.06
3456 9762 9.325198 TGTAAAAGCATCGTAATATTGATCACT 57.675 29.630 0.00 0.00 0.00 3.41
3459 9765 9.547753 AAAAGCATCGTAATATTGATCACTACT 57.452 29.630 0.00 0.00 0.00 2.57
3461 9767 9.627395 AAGCATCGTAATATTGATCACTACTAC 57.373 33.333 0.00 0.00 0.00 2.73
3462 9768 9.015367 AGCATCGTAATATTGATCACTACTACT 57.985 33.333 9.21 0.00 0.00 2.57
3463 9769 9.627395 GCATCGTAATATTGATCACTACTACTT 57.373 33.333 9.21 0.00 0.00 2.24
3466 9772 9.459640 TCGTAATATTGATCACTACTACTTTGC 57.540 33.333 9.21 0.00 0.00 3.68
3467 9773 9.464714 CGTAATATTGATCACTACTACTTTGCT 57.535 33.333 9.21 0.00 0.00 3.91
3488 9794 6.160664 GCTATAAAAAGCACGACTACAACA 57.839 37.500 0.00 0.00 42.30 3.33
3489 9795 6.595794 GCTATAAAAAGCACGACTACAACAA 58.404 36.000 0.00 0.00 42.30 2.83
3490 9796 7.073265 GCTATAAAAAGCACGACTACAACAAA 58.927 34.615 0.00 0.00 42.30 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.386533 CGTTCCTAGGGTCGCTCTTA 58.613 55.000 9.46 0.00 0.00 2.10
17 18 1.753463 CCGTTCCTAGGGTCGCTCT 60.753 63.158 9.46 0.00 0.00 4.09
45 46 2.089349 GTGCAACTCTCCGTCTCGC 61.089 63.158 0.00 0.00 0.00 5.03
91 92 1.227380 GCGACAGTAGGCATGGAGG 60.227 63.158 0.00 0.00 0.00 4.30
341 373 6.377780 ACAAAAACTTGAAAAACATGCAACC 58.622 32.000 0.00 0.00 0.00 3.77
487 1161 3.295093 TCCAAAGTTGCATCTTCAACCA 58.705 40.909 10.38 0.00 45.47 3.67
491 1165 5.787953 TCATTTCCAAAGTTGCATCTTCA 57.212 34.783 10.38 0.00 0.00 3.02
507 1181 2.223805 GGGATGGGCGTTGATTCATTTC 60.224 50.000 0.00 0.00 0.00 2.17
513 1187 1.185315 CTTTGGGATGGGCGTTGATT 58.815 50.000 0.00 0.00 0.00 2.57
573 1247 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
574 1248 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
575 1249 1.755380 CTAATTCCGAACGGAGGGAGT 59.245 52.381 15.34 4.12 46.06 3.85
576 1250 1.755380 ACTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 14.71 46.06 4.30
577 1251 1.856629 ACTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
578 1252 2.277084 CAACTAATTCCGAACGGAGGG 58.723 52.381 15.34 9.70 46.06 4.30
579 1253 2.928116 GACAACTAATTCCGAACGGAGG 59.072 50.000 15.34 10.00 46.06 4.30
580 1254 3.846360 AGACAACTAATTCCGAACGGAG 58.154 45.455 15.34 7.27 46.06 4.63
581 1255 3.671433 CGAGACAACTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
582 1256 2.597305 CGAGACAACTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
583 1257 3.495193 TCGAGACAACTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
584 1258 5.834239 TTTCGAGACAACTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
585 1259 6.128391 CCATTTTCGAGACAACTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
586 1260 5.350365 CCATTTTCGAGACAACTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
587 1261 5.350365 TCCATTTTCGAGACAACTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
588 1262 6.737254 TCCATTTTCGAGACAACTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
589 1263 7.752695 ACATCCATTTTCGAGACAACTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
590 1264 7.687941 ACATCCATTTTCGAGACAACTAATT 57.312 32.000 0.00 0.00 0.00 1.40
591 1265 8.964476 ATACATCCATTTTCGAGACAACTAAT 57.036 30.769 0.00 0.00 0.00 1.73
592 1266 8.258007 AGATACATCCATTTTCGAGACAACTAA 58.742 33.333 0.00 0.00 0.00 2.24
593 1267 7.782049 AGATACATCCATTTTCGAGACAACTA 58.218 34.615 0.00 0.00 0.00 2.24
594 1268 6.644347 AGATACATCCATTTTCGAGACAACT 58.356 36.000 0.00 0.00 0.00 3.16
595 1269 6.910536 AGATACATCCATTTTCGAGACAAC 57.089 37.500 0.00 0.00 0.00 3.32
596 1270 9.443323 TTTTAGATACATCCATTTTCGAGACAA 57.557 29.630 0.00 0.00 0.00 3.18
597 1271 8.879759 GTTTTAGATACATCCATTTTCGAGACA 58.120 33.333 0.00 0.00 0.00 3.41
598 1272 9.099454 AGTTTTAGATACATCCATTTTCGAGAC 57.901 33.333 0.00 0.00 0.00 3.36
627 1301 8.774586 GCAGAAATGGATGTATTTAGACGTATT 58.225 33.333 0.00 0.00 30.78 1.89
628 1302 7.116376 CGCAGAAATGGATGTATTTAGACGTAT 59.884 37.037 0.00 0.00 30.78 3.06
629 1303 6.419710 CGCAGAAATGGATGTATTTAGACGTA 59.580 38.462 0.00 0.00 30.78 3.57
630 1304 5.234329 CGCAGAAATGGATGTATTTAGACGT 59.766 40.000 0.00 0.00 30.78 4.34
631 1305 5.462068 TCGCAGAAATGGATGTATTTAGACG 59.538 40.000 0.00 0.00 30.78 4.18
632 1306 6.844696 TCGCAGAAATGGATGTATTTAGAC 57.155 37.500 0.00 0.00 30.78 2.59
633 1307 9.554395 TTTATCGCAGAAATGGATGTATTTAGA 57.446 29.630 0.00 0.00 43.58 2.10
640 1314 8.299570 GGAATTATTTATCGCAGAAATGGATGT 58.700 33.333 0.00 0.00 43.58 3.06
641 1315 7.482743 CGGAATTATTTATCGCAGAAATGGATG 59.517 37.037 0.00 0.00 43.58 3.51
642 1316 7.390440 TCGGAATTATTTATCGCAGAAATGGAT 59.610 33.333 0.00 0.00 43.58 3.41
643 1317 6.708502 TCGGAATTATTTATCGCAGAAATGGA 59.291 34.615 0.00 0.00 43.58 3.41
644 1318 6.898041 TCGGAATTATTTATCGCAGAAATGG 58.102 36.000 0.00 0.00 43.58 3.16
645 1319 7.058354 CGTTCGGAATTATTTATCGCAGAAATG 59.942 37.037 0.00 0.00 43.58 2.32
646 1320 7.069569 CGTTCGGAATTATTTATCGCAGAAAT 58.930 34.615 0.00 0.00 43.58 2.17
647 1321 6.415702 CGTTCGGAATTATTTATCGCAGAAA 58.584 36.000 0.00 0.00 43.58 2.52
648 1322 5.050634 CCGTTCGGAATTATTTATCGCAGAA 60.051 40.000 5.19 0.00 43.58 3.02
649 1323 4.446385 CCGTTCGGAATTATTTATCGCAGA 59.554 41.667 5.19 0.00 45.75 4.26
650 1324 4.446385 TCCGTTCGGAATTATTTATCGCAG 59.554 41.667 11.66 0.00 0.00 5.18
651 1325 4.370049 TCCGTTCGGAATTATTTATCGCA 58.630 39.130 11.66 0.00 0.00 5.10
652 1326 4.143179 CCTCCGTTCGGAATTATTTATCGC 60.143 45.833 14.79 0.00 33.41 4.58
653 1327 4.387862 CCCTCCGTTCGGAATTATTTATCG 59.612 45.833 14.79 0.00 33.41 2.92
654 1328 5.544650 TCCCTCCGTTCGGAATTATTTATC 58.455 41.667 14.79 0.00 33.41 1.75
655 1329 5.071384 ACTCCCTCCGTTCGGAATTATTTAT 59.929 40.000 14.79 0.00 33.41 1.40
656 1330 4.406649 ACTCCCTCCGTTCGGAATTATTTA 59.593 41.667 14.79 0.00 33.41 1.40
657 1331 3.199289 ACTCCCTCCGTTCGGAATTATTT 59.801 43.478 14.79 0.00 33.41 1.40
658 1332 2.770232 ACTCCCTCCGTTCGGAATTATT 59.230 45.455 14.79 0.00 33.41 1.40
659 1333 2.395619 ACTCCCTCCGTTCGGAATTAT 58.604 47.619 14.79 0.00 33.41 1.28
660 1334 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
661 1335 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
662 1336 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
663 1337 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
664 1338 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
665 1339 1.978454 ATAGTACTCCCTCCGTTCGG 58.022 55.000 0.00 4.74 0.00 4.30
666 1340 2.947652 TCAATAGTACTCCCTCCGTTCG 59.052 50.000 0.00 0.00 0.00 3.95
667 1341 4.796618 GCATCAATAGTACTCCCTCCGTTC 60.797 50.000 0.00 0.00 0.00 3.95
668 1342 3.069729 GCATCAATAGTACTCCCTCCGTT 59.930 47.826 0.00 0.00 0.00 4.44
669 1343 2.628657 GCATCAATAGTACTCCCTCCGT 59.371 50.000 0.00 0.00 0.00 4.69
670 1344 2.628178 TGCATCAATAGTACTCCCTCCG 59.372 50.000 0.00 0.00 0.00 4.63
671 1345 4.689612 TTGCATCAATAGTACTCCCTCC 57.310 45.455 0.00 0.00 0.00 4.30
672 1346 6.402222 CCTATTGCATCAATAGTACTCCCTC 58.598 44.000 19.32 0.00 46.83 4.30
673 1347 5.249393 CCCTATTGCATCAATAGTACTCCCT 59.751 44.000 19.32 0.00 46.83 4.20
674 1348 5.248477 TCCCTATTGCATCAATAGTACTCCC 59.752 44.000 19.32 0.00 46.83 4.30
675 1349 6.360370 TCCCTATTGCATCAATAGTACTCC 57.640 41.667 19.32 0.00 46.83 3.85
676 1350 7.547370 GTCATCCCTATTGCATCAATAGTACTC 59.453 40.741 19.32 6.79 46.83 2.59
677 1351 7.390027 GTCATCCCTATTGCATCAATAGTACT 58.610 38.462 19.32 0.00 46.83 2.73
683 1357 2.816087 GCGTCATCCCTATTGCATCAAT 59.184 45.455 0.00 0.00 37.80 2.57
685 1359 1.543208 GGCGTCATCCCTATTGCATCA 60.543 52.381 0.00 0.00 0.00 3.07
939 1614 4.718961 AGGGCCAATGCTGTACTTTATAG 58.281 43.478 6.18 0.00 37.74 1.31
940 1615 4.788925 AGGGCCAATGCTGTACTTTATA 57.211 40.909 6.18 0.00 37.74 0.98
941 1616 3.669939 AGGGCCAATGCTGTACTTTAT 57.330 42.857 6.18 0.00 37.74 1.40
956 1631 1.338107 GGGGCATTTATACAAGGGCC 58.662 55.000 12.96 12.96 42.92 5.80
1034 1713 3.006940 GCGAACTCATGTTATTGGGTGA 58.993 45.455 0.00 0.00 36.39 4.02
1039 1718 2.930040 AGACCGCGAACTCATGTTATTG 59.070 45.455 8.23 0.00 36.39 1.90
1042 1721 2.230508 AGAAGACCGCGAACTCATGTTA 59.769 45.455 8.23 0.00 36.39 2.41
1191 5629 1.086696 CATGGCAAGAAGTACGTGGG 58.913 55.000 0.00 0.00 0.00 4.61
1196 5634 4.631813 CAGTAGAACCATGGCAAGAAGTAC 59.368 45.833 13.04 4.42 0.00 2.73
1368 5826 7.173218 TGAGAACATTTCCTATGAAGTTGACAC 59.827 37.037 0.00 0.00 0.00 3.67
1771 6286 3.877508 GTGTATTCCCTTGATAGTGGCAC 59.122 47.826 10.29 10.29 0.00 5.01
1827 6342 1.071471 AACTTCGCCACTCCACCTG 59.929 57.895 0.00 0.00 0.00 4.00
2077 6592 4.405358 ACCTTTCCAGCAATGTCAAAAAGA 59.595 37.500 0.00 0.00 0.00 2.52
2580 7114 1.530323 AGTTTGATACACCCGCCAAC 58.470 50.000 0.00 0.00 0.00 3.77
2726 7271 8.297426 CGAGCTGGTATAGAATAGTGAAATGTA 58.703 37.037 0.00 0.00 0.00 2.29
2764 7316 6.654793 TTTCCACAAAACGAAATGAAAAGG 57.345 33.333 0.00 0.00 0.00 3.11
2791 7343 5.419542 TCCTCTCAGGATTACGTTTTCATG 58.580 41.667 0.00 0.00 40.06 3.07
2941 7495 5.713792 ATGTATAGATGGAGTTCTGGACG 57.286 43.478 0.00 0.00 0.00 4.79
3043 7598 0.754217 CATGACCCATCCTTGCCTGG 60.754 60.000 0.00 0.00 0.00 4.45
3046 7601 0.257039 AGACATGACCCATCCTTGCC 59.743 55.000 0.00 0.00 0.00 4.52
3085 7640 7.828712 TGTTTGTCTGATTGAATTATGATGCA 58.171 30.769 0.00 0.00 0.00 3.96
3099 7654 5.813383 AGATCTGAACCATGTTTGTCTGAT 58.187 37.500 0.00 0.00 0.00 2.90
3183 7738 4.985538 TCTTGTCCAGAACTTGCCTAATT 58.014 39.130 0.00 0.00 0.00 1.40
3204 7759 9.076596 GTTATGATGGCAAGTTGTATTCTTTTC 57.923 33.333 4.48 0.00 0.00 2.29
3312 7867 3.230134 AGGACAATAAGCAAGCCACAAA 58.770 40.909 0.00 0.00 0.00 2.83
3377 9682 4.142578 TGTTGTTGCACACTTCACGTTTAT 60.143 37.500 0.00 0.00 0.00 1.40
3391 9696 0.171455 GTCCGGTGTTTGTTGTTGCA 59.829 50.000 0.00 0.00 0.00 4.08
3405 9711 5.240844 GGATGGAACTAAAATATTGGTCCGG 59.759 44.000 0.00 0.00 28.93 5.14
3429 9735 9.586150 GTGATCAATATTACGATGCTTTTACAG 57.414 33.333 0.00 0.00 0.00 2.74
3465 9771 6.160664 TGTTGTAGTCGTGCTTTTTATAGC 57.839 37.500 0.00 0.00 41.59 2.97
3466 9772 9.051027 CATTTGTTGTAGTCGTGCTTTTTATAG 57.949 33.333 0.00 0.00 0.00 1.31
3467 9773 8.775527 TCATTTGTTGTAGTCGTGCTTTTTATA 58.224 29.630 0.00 0.00 0.00 0.98
3468 9774 7.644490 TCATTTGTTGTAGTCGTGCTTTTTAT 58.356 30.769 0.00 0.00 0.00 1.40
3469 9775 7.017498 TCATTTGTTGTAGTCGTGCTTTTTA 57.983 32.000 0.00 0.00 0.00 1.52
3470 9776 5.885881 TCATTTGTTGTAGTCGTGCTTTTT 58.114 33.333 0.00 0.00 0.00 1.94
3471 9777 5.493133 TCATTTGTTGTAGTCGTGCTTTT 57.507 34.783 0.00 0.00 0.00 2.27
3472 9778 5.065988 ACTTCATTTGTTGTAGTCGTGCTTT 59.934 36.000 0.00 0.00 30.89 3.51
3473 9779 4.574828 ACTTCATTTGTTGTAGTCGTGCTT 59.425 37.500 0.00 0.00 30.89 3.91
3474 9780 4.127171 ACTTCATTTGTTGTAGTCGTGCT 58.873 39.130 0.00 0.00 30.89 4.40
3475 9781 4.468095 ACTTCATTTGTTGTAGTCGTGC 57.532 40.909 0.00 0.00 30.89 5.34
3476 9782 6.043327 TCAACTTCATTTGTTGTAGTCGTG 57.957 37.500 6.52 0.00 43.54 4.35
3477 9783 6.092944 TGTTCAACTTCATTTGTTGTAGTCGT 59.907 34.615 6.52 0.00 43.54 4.34
3478 9784 6.482835 TGTTCAACTTCATTTGTTGTAGTCG 58.517 36.000 6.52 0.00 43.54 4.18
3479 9785 8.745837 CATTGTTCAACTTCATTTGTTGTAGTC 58.254 33.333 6.52 0.00 43.54 2.59
3480 9786 8.250332 ACATTGTTCAACTTCATTTGTTGTAGT 58.750 29.630 6.52 0.00 43.54 2.73
3481 9787 8.633075 ACATTGTTCAACTTCATTTGTTGTAG 57.367 30.769 6.52 0.00 43.54 2.74
3482 9788 9.509855 GTACATTGTTCAACTTCATTTGTTGTA 57.490 29.630 0.00 0.00 43.54 2.41
3483 9789 8.250332 AGTACATTGTTCAACTTCATTTGTTGT 58.750 29.630 0.00 0.00 43.54 3.32
3484 9790 8.633075 AGTACATTGTTCAACTTCATTTGTTG 57.367 30.769 0.00 0.00 44.21 3.33
3485 9791 9.730420 GTAGTACATTGTTCAACTTCATTTGTT 57.270 29.630 0.00 0.00 0.00 2.83
3486 9792 8.067784 CGTAGTACATTGTTCAACTTCATTTGT 58.932 33.333 0.38 0.00 0.00 2.83
3487 9793 8.279800 TCGTAGTACATTGTTCAACTTCATTTG 58.720 33.333 0.38 0.00 0.00 2.32
3488 9794 8.373048 TCGTAGTACATTGTTCAACTTCATTT 57.627 30.769 0.38 0.00 0.00 2.32
3489 9795 7.360101 GCTCGTAGTACATTGTTCAACTTCATT 60.360 37.037 0.38 0.00 0.00 2.57
3490 9796 6.090898 GCTCGTAGTACATTGTTCAACTTCAT 59.909 38.462 0.38 0.00 0.00 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.